{"id":"https://openalex.org/W7134060823","doi":"https://doi.org/10.1093/bioinformatics/btag106","title":"PEtab-GUI: a graphical user interface to create, edit, and inspect PEtab parameter estimation problems","display_name":"PEtab-GUI: a graphical user interface to create, edit, and inspect PEtab parameter estimation problems","publication_year":2026,"publication_date":"2026-02-28","ids":{"openalex":"https://openalex.org/W7134060823","doi":"https://doi.org/10.1093/bioinformatics/btag106","pmid":"https://pubmed.ncbi.nlm.nih.gov/41787963"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btag106","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag106","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bioinformatics/btag106","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5000915010","display_name":"Paul Jonas Jost","orcid":"https://orcid.org/0000-0001-7613-6244"},"institutions":[{"id":"https://openalex.org/I135140700","display_name":"University of Bonn","ror":"https://ror.org/041nas322","country_code":"DE","type":"education","lineage":["https://openalex.org/I135140700"]},{"id":"https://openalex.org/I4210164436","display_name":"Life & Brain (Germany)","ror":"https://ror.org/05h6av881","country_code":"DE","type":"company","lineage":["https://openalex.org/I4210164436"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Paul J Jost","raw_affiliation_strings":["Bonn Center for Mathematical Life Sciences, University of Bonn , Bonn 53115,","LIMES Life and Medical Sciences Institute, University of Bonn , Bonn 53115,"],"raw_orcid":"https://orcid.org/0000-0001-7613-6244","affiliations":[{"raw_affiliation_string":"Bonn Center for Mathematical Life Sciences, University of Bonn , Bonn 53115,","institution_ids":["https://openalex.org/I135140700"]},{"raw_affiliation_string":"LIMES Life and Medical Sciences Institute, University of Bonn , Bonn 53115,","institution_ids":["https://openalex.org/I135140700","https://openalex.org/I4210164436"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5128242550","display_name":"Frank T Bergmann","orcid":null},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]},{"id":"https://openalex.org/I85384741","display_name":"Heidelberg University","ror":"https://ror.org/04rcqnp59","country_code":"US","type":"education","lineage":["https://openalex.org/I85384741"]}],"countries":["DE","US"],"is_corresponding":false,"raw_author_name":"Frank T Bergmann","raw_affiliation_strings":["BioQUANT, Heidelberg University , Heidelberg 69120,"],"raw_orcid":"https://orcid.org/0000-0001-5553-4702","affiliations":[{"raw_affiliation_string":"BioQUANT, Heidelberg University , Heidelberg 69120,","institution_ids":["https://openalex.org/I85384741","https://openalex.org/I223822909"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014811978","display_name":"Daniel Weindl","orcid":"https://orcid.org/0000-0001-9963-6057"},"institutions":[{"id":"https://openalex.org/I135140700","display_name":"University of Bonn","ror":"https://ror.org/041nas322","country_code":"DE","type":"education","lineage":["https://openalex.org/I135140700"]},{"id":"https://openalex.org/I4210164436","display_name":"Life & Brain (Germany)","ror":"https://ror.org/05h6av881","country_code":"DE","type":"company","lineage":["https://openalex.org/I4210164436"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Daniel Weindl","raw_affiliation_strings":["Bonn Center for Mathematical Life Sciences, University of Bonn , Bonn 53115,","LIMES Life and Medical Sciences Institute, University of Bonn , Bonn 53115,"],"raw_orcid":"https://orcid.org/0000-0001-9963-6057","affiliations":[{"raw_affiliation_string":"Bonn Center for Mathematical Life Sciences, University of Bonn , Bonn 53115,","institution_ids":["https://openalex.org/I135140700"]},{"raw_affiliation_string":"LIMES Life and Medical Sciences Institute, University of Bonn , Bonn 53115,","institution_ids":["https://openalex.org/I135140700","https://openalex.org/I4210164436"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5128227265","display_name":"Jan Hasenauer","orcid":null},"institutions":[{"id":"https://openalex.org/I135140700","display_name":"University of Bonn","ror":"https://ror.org/041nas322","country_code":"DE","type":"education","lineage":["https://openalex.org/I135140700"]},{"id":"https://openalex.org/I4210164436","display_name":"Life & Brain (Germany)","ror":"https://ror.org/05h6av881","country_code":"DE","type":"company","lineage":["https://openalex.org/I4210164436"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Jan Hasenauer","raw_affiliation_strings":["Bonn Center for Mathematical Life Sciences, University of Bonn , Bonn 53115,","LIMES Life and Medical Sciences Institute, University of Bonn , Bonn 53115,"],"raw_orcid":"https://orcid.org/0000-0002-4935-3312","affiliations":[{"raw_affiliation_string":"Bonn Center for Mathematical Life Sciences, University of Bonn , Bonn 53115,","institution_ids":["https://openalex.org/I135140700"]},{"raw_affiliation_string":"LIMES Life and Medical Sciences Institute, University of Bonn , Bonn 53115,","institution_ids":["https://openalex.org/I135140700","https://openalex.org/I4210164436"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5128227265"],"corresponding_institution_ids":["https://openalex.org/I135140700","https://openalex.org/I4210164436"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.27534931,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"42","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13650","display_name":"Computational Physics and Python Applications","score":0.0778999999165535,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T13650","display_name":"Computational Physics and Python Applications","score":0.0778999999165535,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12505","display_name":"Peptidase Inhibition and Analysis","score":0.03460000082850456,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10522","display_name":"Medical Imaging Techniques and Applications","score":0.013899999670684338,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/modular-design","display_name":"Modular design","score":0.7293000221252441},{"id":"https://openalex.org/keywords/graphical-user-interface","display_name":"Graphical user interface","score":0.7231000065803528},{"id":"https://openalex.org/keywords/estimation-theory","display_name":"Estimation theory","score":0.6543999910354614},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.5422000288963318},{"id":"https://openalex.org/keywords/graphical-display","display_name":"Graphical display","score":0.5291000008583069},{"id":"https://openalex.org/keywords/user-interface","display_name":"User interface","score":0.5135999917984009}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7656000256538391},{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.7293000221252441},{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.7231000065803528},{"id":"https://openalex.org/C167928553","wikidata":"https://www.wikidata.org/wiki/Q1376021","display_name":"Estimation theory","level":2,"score":0.6543999910354614},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.5422000288963318},{"id":"https://openalex.org/C2984927552","wikidata":"https://www.wikidata.org/wiki/Q845734","display_name":"Graphical display","level":2,"score":0.5291000008583069},{"id":"https://openalex.org/C89505385","wikidata":"https://www.wikidata.org/wiki/Q47146","display_name":"User interface","level":2,"score":0.5135999917984009},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.38920000195503235},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3774000108242035},{"id":"https://openalex.org/C96250715","wikidata":"https://www.wikidata.org/wiki/Q965330","display_name":"Estimation","level":2,"score":0.36579999327659607},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.3255000114440918},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.31929999589920044},{"id":"https://openalex.org/C66153210","wikidata":"https://www.wikidata.org/wiki/Q5597182","display_name":"Graphical user interface testing","level":4,"score":0.3077000081539154},{"id":"https://openalex.org/C199639397","wikidata":"https://www.wikidata.org/wiki/Q1788588","display_name":"Engineering drawing","level":1,"score":0.2969000041484833},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.2937000095844269},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.29339998960494995},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.2703000009059906},{"id":"https://openalex.org/C79403827","wikidata":"https://www.wikidata.org/wiki/Q3988","display_name":"Real-time computing","level":1,"score":0.2694000005722046},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.26930001378059387},{"id":"https://openalex.org/C2983447341","wikidata":"https://www.wikidata.org/wiki/Q1413083","display_name":"Model parameter","level":2,"score":0.2606000006198883}],"mesh":[{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btag106","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag106","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41787963","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41787963","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:13012594","is_oa":true,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41787963/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btag106","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag106","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4721312926","display_name":null,"funder_award_id":"W-de.NBI-016","funder_id":"https://openalex.org/F4320330124","funder_display_name":"German Network for Bioinformatics Infrastructure"},{"id":"https://openalex.org/G5473225353","display_name":null,"funder_award_id":"EXC 2151\u2014390873048","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G5709367682","display_name":"MEmilio  Software tools f\u00fcr die modulare r\u00e4umlichzeitliche Modellierung und Simulation von Infektionskrankheitsdynamiken","funder_award_id":"528702961","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G638452479","display_name":null,"funder_award_id":"432325352\u2014SFB 1454","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G717665147","display_name":null,"funder_award_id":"450149205\u2014TRR 333","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G8171175394","display_name":null,"funder_award_id":"EXC 2047\u2014390685813","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320324900","display_name":"Rheinische Friedrich-Wilhelms-Universit\u00e4t Bonn","ror":"https://ror.org/041nas322"},{"id":"https://openalex.org/F4320330124","display_name":"German Network for Bioinformatics Infrastructure","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W2096951208","https://openalex.org/W2102653059","https://openalex.org/W2125615370","https://openalex.org/W2179083909","https://openalex.org/W2950665010","https://openalex.org/W2988361147","https://openalex.org/W3014365047","https://openalex.org/W3080133182","https://openalex.org/W3132502413","https://openalex.org/W3142344196","https://openalex.org/W3204234525","https://openalex.org/W4387652614","https://openalex.org/W4388982138","https://openalex.org/W4390815751","https://openalex.org/W4403371424","https://openalex.org/W4414084902","https://openalex.org/W4416341424"],"related_works":[],"abstract_inverted_index":{"MOTIVATION:":[0],"Parameter":[1],"estimation":[2,38,137],"is":[3,154,172],"a":[4,17,31,100,160,178],"cornerstone":[5],"of":[6,79],"data-driven":[7],"modeling":[8,141],"in":[9,16,145,156],"systems":[10],"biology.":[11],"Yet,":[12],"constructing":[13],"such":[14],"problems":[15,81],"reproducible":[18],"and":[19,42,55,77,96,107,112,124,147,170,183],"accessible":[20],"manner":[21],"remains":[22],"challenging.":[23],"The":[24,164],"PEtab":[25,80,91],"format":[26],"has":[27],"established":[28],"itself":[29],"as":[30,177],"powerful":[32],"community":[33],"standard":[34],"to":[35,60,72,117,131,167],"encode":[36],"parameter":[37,136],"problems,":[39,138],"promoting":[40],"interoperability":[41],"reusability.":[43],"However,":[44],"its":[45],"reliance":[46],"on":[47,174],"multiple":[48],"interlinked":[49],"files-often":[50],"edited":[51],"manually-can":[52],"introduce":[53],"inconsistencies,":[54],"new":[56],"users":[57,116],"often":[58],"struggle":[59],"navigate":[61],"them.":[62],"Here,":[63],"we":[64],"present":[65],"PEtab-GUI,":[66],"an":[67,83],"open-source":[68,158],"Python":[69],"application":[70],"designed":[71,166],"streamline":[73],"the":[74,119,122,125,129],"creation,":[75],"editing,":[76],"validation":[78],"through":[82],"intuitive":[84],"graphical":[85],"user":[86],"interface.":[87],"PEtab-GUI":[88,127,153],"integrates":[89],"all":[90],"components,":[92],"including":[93],"SBML":[94],"models":[95],"tabular":[97],"files,":[98],"into":[99],"single":[101],"environment":[102],"with":[103],"live":[104],"error":[105],"checking":[106],"customizable":[108],"defaults.":[109],"Interactive":[110],"visualization":[111],"simulation":[113],"capabilities":[114],"enable":[115],"inspect":[118],"relationship":[120],"between":[121],"model":[123],"data.":[126],"lowers":[128],"barrier":[130],"entry":[132],"for":[133],"specifying":[134],"standardized":[135],"making":[139],"dynamic":[140],"more":[142],"accessible,":[143],"especially":[144],"educational":[146],"interdisciplinary":[148],"settings.":[149],"AVAILABILITY":[150],"AND":[151],"IMPLEMENTATION:":[152],"implemented":[155],"Python,":[157],"under":[159],"3-Clause":[161],"BSD":[162],"license.":[163],"code,":[165],"be":[168,185],"modular":[169],"extensible,":[171],"hosted":[173],"https://github.com/PEtab-dev/PEtab-GUI,":[175],"available":[176],"Zenodo":[179],"repository":[180],"at":[181],"https://doi.org/10.5281/zenodo.15355752,":[182],"can":[184],"installed":[186],"from":[187],"PyPI.":[188]},"counts_by_year":[],"updated_date":"2026-06-22T08:00:12.763002","created_date":"2026-03-07T00:00:00"}
